Homologous recombination during meiosis is essential for genome integrity in the germ line, but is also a powerful determinant of genome diversity, evolution, and (when mistakes occur) instability. Meiotic recombination is initiated by double-strand breaks (DSBs) made by the Spo11 protein. This proposal addresses molecular mechanisms underlying DSB formation and recombination in the budding yeast, S. cerevisiae. Aims are: 1) To define regulatory mechanisms that ensure that DSBs form after DNA replication. A working model will be tested, in which physical association of a cell cycle regulatory kinase with the replisome targets Mer2 protein for phosphorylation specifically in chromatin that has been replicated. The genome-wide relationship between replication and DSB formation will also be explored. 2) To understand factors that determine DSB distributions. Different genomic regions show different propensity for DSB formation, with this DSB landscape shaped by combinatorial and hierarchical action of many factors. Detailed understanding of these factors is lacking. A novel method for genome-wide mapping of DSBs at nucleotide resolution will be used to determine the contribution of local chromatin structure and of proteins involved in higher-order chromosome folding (cohesins and chromosome axis proteins). Additionally, DSB maps in divergent wild-type laboratory strains will test how DSB distributions vary with genetic background. 3) To determine the relationship between DSB location and gene conversion tracts. Classical tetrad analysis will be combined with state-of-the-art genotyping methods and novel physical assays to map gene conversion tracts with high spatial and quantitative precision around a set of selected DSB hotspots. Comparing these maps to high resolution DSB maps will test predictions of different recombination models. 4) To determine how DSBs in repetitive sequences contribute to genome instability. Recombination between dispersed homologous DNA segments can lead to chromosome rearrangements. Such non-allelic recombination has been extensively studied in yeast meiosis, but usually with artificial repeats. Here, the occurrence of DSBs within and near natural repeats (retrotransposon Ty elements) will be determined using novel genome-wide mapping methods and physical assays. In addition, a new method for detecting and quantifying crossing over between non- allelic Ty elements will be used to determine the extent to which DSBs within Tys contribute to gross chromosomal rearrangements.